Summary

In this part, we are going to visualise the secretory cells after clustering.

It will include the figures we presented in our manuscript.

Visualisation

Scatter plot of secretory clusters

## Warning: 'add_ticks' is deprecated.
## Use '+ geom_rug(...)' instead.

## Warning: 'add_ticks' is deprecated.
## Use '+ geom_rug(...)' instead.

## Warning: 'add_ticks' is deprecated.
## Use '+ geom_rug(...)' instead.

## Warning: 'add_ticks' is deprecated.
## Use '+ geom_rug(...)' instead.

## Warning: 'add_ticks' is deprecated.
## Use '+ geom_rug(...)' instead.

## Warning: 'add_ticks' is deprecated.
## Use '+ geom_rug(...)' instead.

Scatter plots of fresh FTE cells

Plot UMAP of all fresh cells

## 
##  Ciliated Secretory 
##       146      1410
## Warning: 'add_ticks' is deprecated.
## Use '+ geom_rug(...)' instead.

## Warning: 'add_ticks' is deprecated.
## Use '+ geom_rug(...)' instead.

## Warning: 'add_ticks' is deprecated.
## Use '+ geom_rug(...)' instead.

Heatmap

## Warning: The `printer` argument is deprecated as of rlang 0.3.0.
## This warning is displayed once per session.

Violin plots of marker genes

Cluster 4 is characterized by upregulation of major histocompatibility complex (MHC) Class II genes (e.g. HLA-DQA1, HLA-DPA1 and HLA-DPB1), cytokeratins (KRT17, KRT5 and KRT23) and aldehyde dehydrogenases (e.g. ALDH1A1 and ALDH3B2)

## Warning: 'plotPhenoData' is deprecated.
## Use 'plotColData' instead.
## See help("Deprecated")

Technical

## R version 3.5.2 (2018-12-20)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Mojave 10.14.4
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] parallel  stats4    stats     graphics  grDevices utils     datasets 
## [8] methods   base     
## 
## other attached packages:
##  [1] bindrcpp_0.2.2              Seurat_2.3.4               
##  [3] Matrix_1.2-15               cowplot_0.9.4              
##  [5] DoubletFinder_2.0.1         reshape2_1.4.3             
##  [7] scales_1.0.0                dplyr_0.7.8                
##  [9] edgeR_3.24.3                limma_3.38.3               
## [11] scater_1.10.1               ggplot2_3.2.0.9000         
## [13] SingleCellExperiment_1.4.1  SummarizedExperiment_1.12.0
## [15] DelayedArray_0.8.0          BiocParallel_1.16.5        
## [17] matrixStats_0.54.0          Biobase_2.42.0             
## [19] GenomicRanges_1.34.0        GenomeInfoDb_1.18.1        
## [21] IRanges_2.16.0              S4Vectors_0.20.1           
## [23] BiocGenerics_0.28.0        
## 
## loaded via a namespace (and not attached):
##   [1] snow_0.4-3               backports_1.1.3         
##   [3] Hmisc_4.2-0              plyr_1.8.4              
##   [5] igraph_1.2.3             lazyeval_0.2.1          
##   [7] splines_3.5.2            digest_0.6.18           
##   [9] foreach_1.4.4            htmltools_0.3.6         
##  [11] viridis_0.5.1            lars_1.2                
##  [13] gdata_2.18.0             magrittr_1.5            
##  [15] checkmate_1.9.1          cluster_2.0.7-1         
##  [17] mixtools_1.1.0           ROCR_1.0-7              
##  [19] R.utils_2.7.0            colorspace_1.4-0        
##  [21] xfun_0.4                 jsonlite_1.6            
##  [23] crayon_1.3.4             RCurl_1.95-4.11         
##  [25] bindr_0.1.1              zoo_1.8-4               
##  [27] survival_2.43-3          iterators_1.0.10        
##  [29] ape_5.2                  glue_1.3.0              
##  [31] gtable_0.2.0             zlibbioc_1.28.0         
##  [33] XVector_0.22.0           kernlab_0.9-27          
##  [35] Rhdf5lib_1.4.2           prabclus_2.2-7          
##  [37] DEoptimR_1.0-8           HDF5Array_1.10.1        
##  [39] mvtnorm_1.0-8            bibtex_0.4.2            
##  [41] Rcpp_1.0.0               metap_1.1               
##  [43] dtw_1.20-1               viridisLite_0.3.0       
##  [45] htmlTable_1.13.1         reticulate_1.10         
##  [47] foreign_0.8-71           bit_1.1-14              
##  [49] proxy_0.4-22             mclust_5.4.2            
##  [51] SDMTools_1.1-221         Formula_1.2-3           
##  [53] umap_0.1.0.3             tsne_0.1-3              
##  [55] htmlwidgets_1.3          httr_1.4.0              
##  [57] gplots_3.0.1.1           RColorBrewer_1.1-2      
##  [59] fpc_2.1-11.1             acepack_1.4.1           
##  [61] modeltools_0.2-22        ica_1.0-2               
##  [63] pkgconfig_2.0.2          R.methodsS3_1.7.1       
##  [65] flexmix_2.3-14           nnet_7.3-12             
##  [67] dynamicTreeCut_1.63-1    locfit_1.5-9.1          
##  [69] labeling_0.3             tidyselect_0.2.5        
##  [71] rlang_0.4.0              munsell_0.5.0           
##  [73] tools_3.5.2              ggridges_0.5.1          
##  [75] evaluate_0.13            stringr_1.4.0           
##  [77] yaml_2.2.0               npsurv_0.4-0            
##  [79] knitr_1.21               bit64_0.9-7             
##  [81] fitdistrplus_1.0-14      robustbase_0.93-3       
##  [83] caTools_1.17.1.1         purrr_0.3.0             
##  [85] RANN_2.6.1               pbapply_1.4-0           
##  [87] nlme_3.1-137             scran_1.10.2            
##  [89] R.oo_1.22.0              hdf5r_1.0.1             
##  [91] compiler_3.5.2           rstudioapi_0.9.0        
##  [93] png_0.1-7                beeswarm_0.2.3          
##  [95] lsei_1.2-0               statmod_1.4.30          
##  [97] tibble_2.0.1             stringi_1.2.4           
##  [99] lattice_0.20-38          trimcluster_0.1-2.1     
## [101] pillar_1.3.1             lmtest_0.9-36           
## [103] Rdpack_0.10-1            BiocNeighbors_1.0.0     
## [105] data.table_1.12.0        bitops_1.0-6            
## [107] irlba_2.3.3              gbRd_0.4-11             
## [109] R6_2.3.0                 latticeExtra_0.6-28     
## [111] KernSmooth_2.23-15       gridExtra_2.3           
## [113] vipor_0.4.5              codetools_0.2-16        
## [115] MASS_7.3-51.1            gtools_3.8.1            
## [117] assertthat_0.2.0         rhdf5_2.26.2            
## [119] withr_2.1.2              GenomeInfoDbData_1.2.0  
## [121] diptest_0.75-7           doSNOW_1.0.16           
## [123] grid_3.5.2               rpart_4.1-13            
## [125] tidyr_0.8.2              class_7.3-15            
## [127] rmarkdown_1.11           DelayedMatrixStats_1.4.0
## [129] segmented_0.5-3.0        Rtsne_0.15              
## [131] base64enc_0.1-3          ggbeeswarm_0.6.0